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  #1  
Old 14th March 2017, 04:26 PM
RN1 RN1 is offline
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Question I Was... Z17! - But Now, After The Big Y, I Am... ZP158 !... Question:

I have just received my Big Y results and my Haplogroup has changed from confirmed ‘Tested Positive’ R-Z17 to confirmed ‘Tested Positive’ R-ZP158.

R-ZP158 is downstream of R-Z372 as are R-ZP159, R-ZP160 & R-ZP161, all of which I have 'Tested Positive'.

Can anyone ( MMaddi ) tell me if R-ZP158 is either upstream or downstream of R-ZP159, R-ZP160 & R-ZP161 ?

All this upstream-downstream business is too much for a R-ZP158'er...
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Old 14th March 2017, 09:35 PM
MMaddi MMaddi is offline
yDNA: R-CTS2509; mtDNA: T2e
 
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I checked on FTDNA's yDNA haplotree, which is found in the account of anyone who's tested yDNA. I searched for the various ZP SNPs that you mentioned. I don't find any of them in the FTDNA tree.

Then I checked the latest Big Y analysis spreadsheet issued today by Iain McDonald, a co-administrator of the R1b-U106 Project. The spreadsheet has 5 men who are positive for ZP158, ZP159, ZP160, S5970, ZP161, S5960 and S5965. It looks like these 7 SNPs are equivalent. Basically, that means that everyone who's positive for one of them is also positive for the other 6; they all define the same subclade. Iain's estimate is that S5970 was "born" about 306 AD (with a range of 444 BC — 891 AD).

Going back to the FTDNA tree, I searched for S5970, S5960 and S5965. I couldn't find the last two on the tree, but S5970 is there. It has ZP158, ZP159, ZP160 and ZP161 listed as equivalent SNPs. They are a subclade of (downstream from) ZP91 and they have their own subclade, defined by S7019.

This probably means that you're negative for S7019. Are you negative for S5970, S5960 and S5965? If you are negative for any of S5970, S5960 and S5965, then that means the one(s) you're negative for are downstream from the ZP SNPs you mentioned.

Also, I don't see your Big Y results in the R1b-U106 Project. Have you joined that yet? If not, please do so. We can include your Big Y results in our analysis spreadsheet and add a new subclade, if necessary. Having a sixth person for this subclade will also help make the age estimate more accurate.

Last edited by MMaddi; 14th March 2017 at 09:48 PM.
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Old 16th March 2017, 12:31 PM
RN1 RN1 is offline
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Thumbs up MMaddi - Simply The Best!

As always MMaddi, thank you for your amazing response and answers. It is always a pleasure reading your replies.

Quote:
Originally Posted by MMaddi View Post
I checked on FTDNA's yDNA haplotree, which is found in the account of anyone who's tested yDNA. I searched for the various ZP SNPs that you mentioned. I don't find any of them in the FTDNA tree.

Then I checked the latest Big Y analysis spreadsheet issued today by Iain McDonald, a co-administrator of the R1b-U106 Project. The spreadsheet has 5 men who are positive for ZP158, ZP159, ZP160, S5970, ZP161, S5960 and S5965. It looks like these 7 SNPs are equivalent. Basically, that means that everyone who's positive for one of them is also positive for the other 6; they all define the same subclade. Iain's estimate is that S5970 was "born" about 306 AD (with a range of 444 BC — 891 AD).

Going back to the FTDNA tree, I searched for S5970, S5960 and S5965. I couldn't find the last two on the tree, but S5970 is there. It has ZP158, ZP159, ZP160 and ZP161 listed as equivalent SNPs. They are a subclade of (downstream from) ZP91 and they have their own subclade, defined by S7019.

This probably means that you're negative for S7019. Are you negative for S5970, S5960 and S5965? If you are negative for any of S5970, S5960 and S5965, then that means the one(s) you're negative for are downstream from the ZP SNPs you mentioned.

Also, I don't see your Big Y results in the R1b-U106 Project. Have you joined that yet? If not, please do so. We can include your Big Y results in our analysis spreadsheet and add a new subclade, if necessary. Having a sixth person for this subclade will also help make the age estimate more accurate.
Can you indulge me further by answering more questions?

Strangely, on FTDNA's yDNA haplotree on my account, ZP91 is only listed as ’Presumed Positive’ (written in light brown/beige) yet I have ‘Tested Positive’ for Z372 (written in green) which is upstream of ZP91 and, as mentioned before, ‘Tested Positive’ for ZP158 (written in green) which is downstream of ZP91. I wonder why ZP91 is not showing up as ‘Tested Positive’?

This is also the case for S5970 – again showing in the same light brown/beige colour as ZP91 - ‘Presumed Positive’. I have, however, ‘Tested Positive’ for S5960 and S5965. Do you have any idea why this is?

You are absolutely correct – I ‘Tested Negative’ for S7019.

As you say early in your reply, that it looks like the seven SNPs ZP158, ZP159, ZP160, S5970, ZP161, S5960 and S5965 are equivalent, but do we know in which order they were discovered? If I have ‘Tested Positive’ (or ‘Presumed Positive in the case of S5970) for all of these, what determines that I am ZP158 and not any of the other six? (Is it something to do with Novel Variants?)

I have not as yet joined the R1b-U106 Project but I hope to request to do so very shortly. I may have a few questions regarding joining before I do.

Many thanks again.

Last edited by RN1; 16th March 2017 at 12:33 PM. Reason: Word omitted
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Old 16th March 2017, 05:22 PM
MMaddi MMaddi is offline
yDNA: R-CTS2509; mtDNA: T2e
 
Join Date: Jul 2005
Location: Houston, TX
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Quote:
Originally Posted by RN1 View Post
Strangely, on FTDNA's yDNA haplotree on my account, ZP91 is only listed as ’Presumed Positive’ (written in light brown/beige) yet I have ‘Tested Positive’ for Z372 (written in green) which is upstream of ZP91 and, as mentioned before, ‘Tested Positive’ for ZP158 (written in green) which is downstream of ZP91. I wonder why ZP91 is not showing up as ‘Tested Positive’?

This is also the case for S5970 – again showing in the same light brown/beige colour as ZP91 - ‘Presumed Positive’. I have, however, ‘Tested Positive’ for S5960 and S5965. Do you have any idea why this is?
Those that are "presumed positive" probably did not have enough clear calls in your Big Y results for FTDNA to make a definite positive call. However, since you have confident positive calls for the upstream SNP (Z372) and the downstream SNPs (ZP158, etc.), FTDNA legitimately assumes that you are positive for ZP91 and S5970. It's possible, but very unlikely, that you have had back mutations at ZP91 and/or S5970, so FTDNA presumes that you are positive for the string of SNPs in the subclade you're in, which would be ZP91+ and S5970+. Your Big Y raw data (the combined VCF and BED files, not the BAM file) gives you information about what calls for which SNPs they had sufficient coverage to make confident calls.

Quote:
Originally Posted by RN1 View Post
As you say early in your reply, that it looks like the seven SNPs ZP158, ZP159, ZP160, S5970, ZP161, S5960 and S5965 are equivalent, but do we know in which order they were discovered? If I have ‘Tested Positive’ (or ‘Presumed Positive in the case of S5970) for all of these, what determines that I am ZP158 and not any of the other six? (Is it something to do with Novel Variants?)
There's no way to know the order in which the SNPs occurred until someone tests positive for 4 or 5 or 6 of the SNPs and negative for the others. It may be that there's no S5970+ paternal line existing today who is in that situation. In that case, there would be no way to tell the order of the SNPs.

More Big Y results from the S5970 subclade would be about the only way we'll ever know. The other option is that more refined results would come from analysis of BAM files of Big Y results from your subclade by two other companies (FGC or YFull, both charge $50 for the service) that offer to analyze BAM files for SNP calls that FTDNA didn't make. FGC also offers its own test, YElite, which covers several million more yDNA locations than Big Y does and can find SNPs that Big Y doesn't cover.

Frankly, it doesn't make much sense that FTDNA's tree names your subclade in their tree as S5790, yet says your personal subclade is Z158. Maybe it's because they didn't get enough clear calls that you're S5790+, so went with Z158, since that's an equivalent SNP for which they could make a clear call. Unfortunately, given all the equivalent SNPs in the tree and the fact that FTDNA and even the haplogroup projects are always playing catch-up in having a consistent, up to date tree, it is confusing, especially when there are so many equivalent SNPs for many subclades.

Quote:
Originally Posted by RN1 View Post
I have not as yet joined the R1b-U106 Project but I hope to request to do so very shortly. I may have a few questions regarding joining before I do.

Many thanks again.
If you have any questions about the project, just ask. If you'd rather not post them publicly here, send me a private message.

You can also join our associated Yahoogroup by sending a join request to r1b1c_u106-s21-subscribe@yahoogroups.com. You can ask questions there and discuss your results. We also ask those who are U106+ and have Big Y results to upload their VCF/BED files to the group files section so that we can include it in our Big Y analysis spreadsheet. That will tell you and us with whom you share one or more of your novel variants, which may create a new subclade. In order to have access to the files section, you must either join using a Yahoo e-mail address or another address that you've associated with a free Yahoo account.

Last edited by MMaddi; 16th March 2017 at 05:36 PM.
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